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Atlas from human brain structures to 3D coordinates?

Atlas from human brain structures to 3D coordinates?



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I would like to visualize specific human brain structures in the three dimensional space and compute specific geometric properties of these brain structures (size, centroid, etc).

Therefore, I am looking for an atlas that maps human brain structures to 3D coordinates (in Talairach or MNI coordinates).

I saw online a lot of websites allowing the inverse mapping, which is from coordinates to brain structures. So I know that this data should be somewhere but I was not able to find it.

Any lead would be greatly appreciated.


Atlas from human brain structures to 3D coordinates? - Biology

The Brain Explorer 2 software is a desktop application for viewing the human brain anatomy and gene expression data in 3-D. Using the Brain Explorer 2 software, you can:

  • View a fully interactive version of the Allen Human Brain Atlas in 3-D.
  • View gene expression data in 3-D: inflated cortical surfaces are colored by gene expression values of nearby samples.
  • View expression data from different donors side-by-side.
  • Explore anatomically-labeled MRI images and cortical surfaces.
  • Investigate probes or samples of interest in more detail with direct links back to the Allen Human Brain Atlas web page.

After installing the Brain Explorer 2 software, you can view gene expression data by performing a gene search from the Microarray page or from within the application's main window. Please see the documentation for more information.

Please verify your system meets the requirements before installing.

Windows Minimum Configuration

  • Operating System: Microsoft Windows 7
  • CPU: Intel Core Duo or AMD 1.8GHz
  • System Memory: 1GB
  • Graphics Card: Hardware 3D OpenGL accelerated AGP or PCI Express with 64MB RAM
  • Screen: 1024x768, 32-bit true color
  • Hard Disk: 200MB free space

Note: The Brain Explorer 2 software is known to work with the following video chipsets: nVidia GeForce 9400/9600, nVidia Quadro FX 1800/3800/5600, AMD Radeon 9600, AMD Radeon HD 3200/4550, Intel Q35/Q45 Express

Important: Please install the latest drivers for your video card for best compatibility and performance.

Mac Minimum Configuration

  • Operating System: OS X 10.6.8
  • CPU: Intel 1.8GHz
  • System Memory: 1GB
  • Graphics Card: 3D-capable with 64MB RAM
  • Screen: 1024x768, 32-bit millions of colors
  • Hard Disk: 200MB free space

Note: Please install the latest system updates from Apple to ensure you have the latest video card drivers.


Experimental Analysis of Behavior, Part 2

2.1 Stereotaxic techniques

The use of stereotaxic instruments and stereotaxic atlases has been reviewed by Pellegrino and Cushman (1971) . These authors also provide a list of additional references for stereotaxic atlases for use with several different species. Satisfactory histological methods for examining and locating the sites for cannula placement, extent of damage etc. also must be available once the particular study has been completed. These topics are treated in some detail in several specific texts in addition to the Pellegrino and Cushman article and should be consulted prior to embarking on studies of the nature described in this chapter (see also Bures et al., 1983 Joseph and Waddington, 1986 ).


  • Preface
    • Part 1: Three Atlases of the Brain in the Head
    • Part 2: Atlas of the Human Brain in Stereotaxic (MNI) Space (AHB)
    • Reproduction of Figures by Users of the Atlas
    • Acknowledgements
    • Part 1: Three Atlases of the Brain in the Head
    • 1.1: Materials and Methods
      • 1.1.1 Anatomical Preparations
      • 1.1.2 Magnetic Resonance Imaging (MRI)
      • 1.1.3 Preparation and Photography of the Anatomical Slices
      • 1.1.4 Preparation of 100 μm Thick Frozen Histological Brain Sections
      • 1.1.5 Presentation of the Images for the Three Atlases of the Brain in the Head
      • 2.1: Material and Methods
        • 2.1.1 The Brain
        • 2.1.2 Methods
        • 2.1.3 Earlier Histological, Morphometric and Immunohistochemical Studies
        • 2.1.4 Nomenclature
        • 2.1.5 Photographic Plates and Corresponding Diagrams
        • 2.1.6 Three-Dimensional Reconstructions
        • 2.1.7 Standardization
        • 2.1.8 Mapping of the Atlas Space to the Talairach-Space
        • 2.1.9 Mapping of the Atlas Space to the MNI/ICBM2009b Template
        • 2.1.10 AHB Reconstruction with MNI/ICBM2009b Shape Constrain
        • 2.1.11 Registration of the Histological Sections to the Reconstructed Volume
        • 2.1.12 Use of the Atlas for the Interpretation of Individual in vivo Brains
        • 2.1.13 Mapping of the Cortex Areas
        • 2.1.14 Generation of the Linear Representation of Cortex “Stripes”
        • 2.1.15 The Layout of the Myelo- and Cytoarchitectonic Stereotaxic Atlas in MNI Space
        • 2.5.1 Thalamus by F. Forutan
        • 2.5.2 Hypothalamus by Y. Koutcherov
        • 2.6.1 Histological, Morphometric and Histochemical Studies

        Juergen Mai

        Jürgen Konrad Mai studied medicine in Freiburg, Germany, Vienna and UT Southwestern Medical School, Dallas, U.S.A. Student and Medical practices in Freiburg (Clinic for Neurosurgery), Berlin and Düsseldorf. Dissertation ("summa cum laude") and habilitation were awarded by the University of Düsseldorf: After a period as GP in private practice (Titisee-Neustadt) he became scientific assistant and senior assistant at the C. and O. Vogt-Institute for Brain Research, University of Düsseldorf (1972 - 1983) and 1983 Professor of Neuroanatomy at the Institute of Neuroanatomy, H.-Heine-University of Düsseldorf. He served as director of the Department of the Institute of Anatomy 1 until retirement in 2011.

        The main research interests are (i) the structural and molecular anatomy of the mammalian brain, especially of the human brain and (ii) expression patterns and regulation of terminal carbohydrates in development, cell activation and disease (III) operation planning in stereotactic neurosurgery. He works on a "Digital Brain Atlas for Planning and Interindividual Registration of Targets in Deep Brain Stimulation" and on a "Spatial Information Management Resource for the Human Brain". J. K. Mai has edited the catalogue of human brain sections from the Vogt collection he is author and editor of several books, e.g. the awarded "Atlas of the Human Brain" with CD-ROM (Academic Press/Elsevier, San Diego), "The Human Nervous System" (Academic Press/Elsevier, San Diego, Amsterdam, 3rd ed. 2012), Funktionelle Anatomie für Zahnmediziner (Quintessenz, Berlin, 2nd. ed. 2008 Sensi Divini (ital., engl., ger, russ. eds). J. K. Mai is CEO of MR-X-Brain GmbH.

        Affiliations and Expertise

        Institute of Anatomy I, Heinrich-Heine-University, Düsseldorf, Germany

        Milan Majtanik

        Milan Majtanik received his diploma in neuropsychology and training in neuroinformatics from the University of Bochum. He completed his diploma in mathematics and his PhD in psychology at the University of Düsseldorf. In his research at the Research Center Jülich he combined advanced analysis techniques in magnetoencephalography (synchronization tomography) with computational modelling in order to measure the impact of desynchronizing sensory stimulation on brain functions. His work on neural plasticity and desynchronizing neural stimulation provided framework for the developent of novel therapeutic techniques. He is currently focusing on the development of novel algorithms for high precision mapping and analysis of individual MRI scans.

        Affiliations and Expertise

        MR-X-Brain GmbH, Düsseldorf, Germany

        George Paxinos

        Professor George Paxinos, AO (BA, MA, PhD, DSc) completed his BA at The University of California at Berkeley, his PhD at McGill University, and spent a postdoctoral year at Yale University. He is the author of almost 50 books on the structure of the brain of humans and experimental animals, including The Rat Brain in Stereotaxic Coordinates, now in its 7th Edition, which is ranked by Thomson ISI as one of the 50 most cited items in the Web of Science. Dr. Paxinos paved the way for future neuroscience research by being the first to produce a three-dimensional (stereotaxic) framework for placement of electrodes and injections in the brain of experimental animals, which is now used as an international standard. He was a member of the first International Consortium for Brain Mapping, a UCLA based consortium that received the top ranking and was funded by the NIMH led Human Brain Project. Dr. Paxinos has been honored with more than nine distinguished awards throughout his years of research, including: The Warner Brown Memorial Prize (University of California at Berkeley, 1968), The Walter Burfitt Prize (1992), The Award for Excellence in Publishing in Medical Science (Assoc Amer Publishers, 1999), The Ramaciotti Medal for Excellence in Biomedical Research (2001), The Alexander von Humbolt Foundation Prize (Germany 2004), and more.

        Affiliations and Expertise

        Neuroscience Research Australia and The University of New South Wales, Sydney, Australia


        Atlases

        An atlas of the brain allows us to define its spatial characteristics. Where is a given structure relative to what other features what are its shape and characteristics and how do we refer to it? Where is this region of functional activation? How different is this brain compared with a normal database? An atlas allows us to answer these and related questions quantitatively. Brain atlases are built from one or more representations of brain. They describe one or more aspects of brain structure and/or function and their relationships after applying appropriate registration and warping strategies, indexing schemes and nomenclature systems. Atlases made from multiple modalities and individuals provide the capability to describe image data with statistical and visual power.

        Brain atlases are built from one or more representations of brain. They describe one or more aspects of brain structure and/or function and their relationships after applying appropriate registration and warping strategies, indexing schemes and nomenclature systems. Atlases made from multiple modalities and individuals provide the capability to describe image data with statistical and visual power.

        An atlas can take on many forms, from descriptions of structure or function of the whole brain to maps of groups or populations. Individual systems of the brain can be mapped as can changes over time, as in development or degeneration. An atlas enables comparison across individuals, modalities or states. Differences between species can be catalogued. But in most cases, the value added by brain atlases is the unique and critical ability to integrate information from multiple sources. The utility of an atlas is dependent upon appropriate coordinate systems, registration and deformation methods along with useful visualization strategies. Accurate and representative atlases of brain hold the most promise for helping to create a comprehensive understanding of brain in health and disease.

        Disclaimer: All Brain atlases available from this site are distributed in good faith and to the best of our knowledge accurately represent brain structure, function and physiology. However, everyone downloading and using any of these atlases agrees to use them under the usage terms and acknowledges that the use of these atlases is at their own risk. Always check the accuracy of any results you obtain using these atlases. The atlases are NOT FDA Approved for clinical/health applications.

        Alzheimer's Disease Template

        The AD atlas is designed to reflect the unique anatomy and physiology of the clinical subpopulation suffering from Alzheimer's disease. The atlas acts as a quantitative framework that correlates the structural, metabolic, molecular and histologic hallmarks of the disease. Additional algorithms are described that use information stored in the atlas to recognize anomalies and label structures in new patients. With the information on group anatomical variability, disease-specific atlases are a type of probabilistic atlas specialized to represent a particular clinical group. The resulting atlas can identify patterns of altered structure or function, and can guide algorithms for knowledge-based image analysis, automated image labeling, tissue classification, and functional image analysis. Since current brain templates poorly represent the anatomy of this clinical population, the resulting atlas offers a framework to investigate the disease. Pathological change can be tracked over time, and disease-specific features resolved. Rather than simply fusing information from multiple subjects and sources, new mathematical strategies are introduced to resolve group-specific features not apparent in individual scans. Corrected for 2015.

        This Archive is composed of three main groups: children, adults, and elderly subjects, which are further subdivided into Normal Controls and Diseased populations. The disease varies per group, with diseased children, suffering from ADHD, the adults, suffering from Alzheimer's, and the elderly, having dementia. Under each of these directories, both male and female subjects can be found, each containing at least 3 subjects. To be inclusive of variations most commonly found in data-sets and potential effects which they may have on existing programs, work was done in both Native (scanner) space and after alignment to ICBM space (12 parameters). A diagrammatic description of the organization of the data in this archivecan be found at . We started with the raw volumes of 36 subjects and ended with close to 1,400 volumes of processed data.

        Future efforts will involve the delineation of other sub-cortical structures, the acquisition of one subject having gone through multiple protocols and sequences, tissue classification using visual verification and manual touching up of each slice by an individual, in an effort to ensure that tissue is being classified correctly.

        Future efforts will involve the delineation of other sub-cortical structures, the acquisition of one subject having gone through multiple protocols and sequences, tissue classification using visual verification and manual touching up of each slice by an individual, in an effort to ensure that tissue is being classified correctly.

        Chinese brain Atlas is an average brain template composed of high quality brain MRI data from 56 Chinese young subjects. Seven additional Chinese brains were registered to both ICBM152 and the Chinese_56 atlas. It is found that there is more deformation required to register the additional Chinese brains to the ICBM152 than to the Chinese_56. Thus the Chinese brain template (Chinese_56) better represents the shape and size of the Chinese population.

        For the localization of activated regions identified by functional imaging an overlay with an anatomical atlas is required. However, there is considerable intersubject structural variability, caused by different macroscopical anatomy, as reflected by a different sulcus pattern, and by different location and extent of cortical areas, which can only be defined microscopically. Therefore, only the spatial normalization of the macroscopical anatomy of an MRI brain dataset to a common reference system permits statements about the structural intersubject variability of architectonic areas and their correlation to functional activations.

        In Juelich and Duesseldorf (http://www.fz-juelich.de/ime/) cytoarchitectonic areas have already been analyzed and spatially normalized to ECHBD space. The ICBM 452 space is used within the ICBM consortium and large parts of the neuroscientific community for functional data analysis. Maps of the motor and somatosensory cortex, the auditory cortex, the visual cortex and Broca’s region, and fiber tracts have already been published. However, within SPM, widely used for functional data analysis, brains are normalized to ICBM 452 space. Preceding studies showed the benefit of an overlay of cytoarchitectonic maps and SPM data. Therefore the transformation of the cytoarchitectonic maps into the MNI space is desirable for an easy structural-functional analysis.

        Fetal brain atlas were built from 7.0T MRI data of 34 postmortem human fetal brains with gestational ages ranging from 15 to 22 weeks. This atlas dataset include atlases of each gestational week and the overall atlas covering the whole period. Advanced normalization tools (ANTS) was used to built these symmetric group-wise atlases. Tensor-based morphology (TBM) and local shape analysis (LSA) were performed based on the atlases. The dataset includes:

        &bull atlases of each week and the overall atlas
        &bull extracted surface of each atlases
        &bull Jacobian determinant of transformation during atlas built
        &bull local shape analysis results after surface registration

        The Human atlas is a spatially accurate, high-resolution three-dimensional (3D) volume of brain anatomy from cryosectioned whole human head. The head of a 76 year old female cadaver was cryosectioned on a heavy duty cryomacrotome (PMV, Stockholm Sweden) modified for quantitative digital image capture. Data were placed into the Talairach coordinate system to create a volume of brain anatomy for atlas reference. The spatial resolution of the original digitized images provided sufficient anatomic detail to clearly delineate gray and white matter and neural structures, including major fiber pathways, subthalamic nuclei, and laminae. Animation proved useful in the conveyance of system anatomy as structures are shown traversing through the neuroaxis. Postmortem cryosectioning paired with this computerized presentation allowed the complete 3D volume data to be distributed and shared as an educational, clinical, and research resource.

        The ICBM452 atlas is an average of T1-weighted MRIs of normal young adult brains. The space the atlas is in is not based on any single subject. Instead it is an average space constructed from the average position, orientation, scale, and shear from all the individual subjects. The atlas, therefore, is both an average of intensities and of spatial positioning.

        The ICBM DTI-81 Atlas is a stereotaxic probabilistic white matter atlas that fuses DTI-based white matter information with an anatomical template (ICBM-152). This atlas is based on probabilistic tensor maps obtained from 81 normal subjects acquired under an initiative of the International Consortium of Brain Mapping (ICBM). The subjects were normal right-handed adults ranging from 18 to 59 years of age. A hand-segmented white matter parcellation map was created from this averaged map. This map can be used for automated white matter parcellation. The precision of the affine-based image normalization and automated parcellation was measured for a group of normal subjects using manually defined anatomical landmarks.

        ICBM Probabilistic Atlases

        The ICBM452 atlas is an average of T1-weighted MRIs of normal young adult brains. The space the atlas is in is not based on any single subject. Instead it is an average space constructed from the average position, orientation, scale, and shear from all the individual subjects. The atlas, therefore, is both an average of intensities and of spatial positioning.

        The ICBM T2 50 atlas is an average of the T2-weighted MRIs of 50 normal young adult brains (equal gender distribution). The space the atlas is based on is the ICBM 452 deterministic atlas and not on any single subject. It represents the mean volume constructed from the average position, orientation, scale, and shear from all 50 individual subjects. The atlas, therefore, is both an average of T2 intensities as well as spatial positioning.

        The purpose of the ICBM brain template is to provide a reference that includes both a set of coordinates and the associated anatomical labels. The localization of functional imaging results on averages of large number of brain MRI volumes does not provide detailed anatomical information. Alternatively, the spatial registration and normalization of brain images from different individuals to a single high-resolution labeled template recognizes the topographically relevant anatomical substrate for a specific activation.

        The ICBM (International Consortium for Brain Mapping) high-resolution single subject template is aligned with the individual subject T1 whole brain MRI provided. An AIR nonlinear warp, a 5th order polynomial, is used for this fit. The demarcated labels on the template are then resampled through the warp transform to the subject MRI. A nearest-neighbor resampling is used to ensure the labels stay as labels. The 0.125mm3 resolution of the template helps ensure that the proper label, at least according to the transform, is used in the resampling.

        The volumes are in minc format and can presently be visualized using the program Display. To view both the structural MRI and the labels launch the program typing Display icbm_template.mnc -label icbm_labels_corrected.mnc. The opacity of the labels can be set in the Colour Coding menu. The number of each label appears at the bottom left of the orthogonal views window. This number corresponds to a unique structure as listed in the table provided (labels_text).

        • Intensity averages of the co-registered skull-stripped MRI volumes.
        • Probabilistic tissue maps based on automated classification of the native-space MRI into white matter, grey matter, and cerebrospinal fluid.
        • Probabilistic maps for each delineated structure.
        • Probabilistic maps for the grey matter portions of each structure.
        • Maximum likelihood maps that identify the most likely structure at each voxel in the atlas space.

        Publications

        Please cite this article as: Shattuck DW, Mirza M, Adisetiyo V, Hojatkashani C, Salamon G, Narr KL, Poldrack RA, Bilder RM, Toga AW, Construction of a 3D Probabilistic Atlas of Human Cortical Structures, NeuroImage (2007), doi: 10.1016/j.neuroimage.2007.09.031

        A three-dimensional multimodality computerized map of the nemestrina monkey brain was created with serial sectioning and digital imaging techniques. An adult female Macaca nemestrina (pigtail macaque) weighing 7.2 kg was used in constructing this atlas. CT, PET, MRI and Cryo data were gathered on the subject. Whole head and brain only 3D image sets were created from the specimen blockface. The CT, PET, and MRI data sets were reconstructed into a digital volume and co-registered (CT and MRI by landmark matching and fiducials, PET by an automated ratio method) to the cryosection volume. The CT, PET, and MRI data sets were reconstructed into a digital volume and co-registered (CT and MRI by landmark matching and fiducials, PET by an automated ratio method) to the cryosection volume.

        The MAP atlas is comprised of a magnetic resonance microscopy (MRM) and an anatomic delineation volume, and a set of software tools for visualization, navigation, and registration of image volumes. The MRM volume is a diffusion-weighted image (DWI) acquired over several hours in a high-field magnet. DWI volumes show a great deal of anatomical detail and good contrast between gray and white matter. Anatomic delineations serve to help orient the user with graphical representations highlighting important anatomical detail and providing a standard description and nomenclature of the region of interest. The anatomical parcellation is based on Brain Maps (Swanson, 1998) with modifications to adapt it to mouse neuroanatomy. The delineations are overlaid upon the MRM volume for visualization.

        Mouse Magnetic Resonance Microscopy Atlas

        An atlas based on a magnetic resonance microscopy (MRM) image diffusion-weighted in the Z-direction acquired from a normal, 100-day old male C57BL/6J mouse. The atlas is comprised of a diffusion-weighted image volume, a label volume, a mask volume, and a label index.

        Mouse Minimum Deformation Atlas

        This atlas is constructed from T2-weighted magnetic resonance microscopy (MRM) images acquired from 11 normal female C57BL/6J mice and is the default atlas for the Mouse BIRN Atlasing Toolkit (MBAT).

        Neonatal (P0) Mouse Nissl Brain Atlas

        A full-color Nissl-stained volume with resolution of 6.6 x 50 x 6.6 µm 3 was constructed. A sub-sampled version of this volume (with resolution of 13.3 x 50 x 13.3 µm 3 ) was co-registered to a standard anatomical space defined by an averaged geometry of C57BL/6J P0 mouse brains. A hundred and forty-five anatomical structures were delineated based on the histological images. Anatomical relationships of delineated structures were established based on the hierarchical relations defined in the atlas of adult mouse brain so the P0 atlas can be related to the database associated with the adult atlas.

        Neonatal (P0) MRI Mouse Brain Atlas

        The atlas was constructed from the average of eight individual co-registered MR image volumes of C57BL/6J mouse brain collected at postnatal day 0. The atlas space defined by multi animals captured the average geometry of native anatomical space for normal mouse brains at P0, avoiding possible anatomical outliers present in one animal. The label volume based on this average brain is consisted of 13 anatomic structures, which provides a template to facilitate feature-based registration. The probability maps for individual anatomical volumes were defined by the eight -registered MR images used to construct the atlas, which serve as references to map the atlas onto test images and to label the regions of interest of test images. The probability map with a restrictive threshold provides a more accurate mapping, while that with lower threshold labels an image more completely.

        The atlas is comprised of:

        1. an image volume of the average brain.
        2. an anatomical label volume ( 13 structures)based on the average brain, and anatomical label volumes ( 13 structures ) retrieved from the probability maps at threshold of 62.5%, 75%, 87.5% and 100% confidences estimated from the population used to construct the atlas ( all structures here are smaller then the sizes of their corresponding average structures ). The names of the structures can be referenced from their intensities of the label volumes with the index table provided.
        3. probability maps for each of the 13 anatomical structures. The probability values in space were encoded with intensities.
        4. sub-volumes for each anatomical structure tessellated from anatomical label volumes described in 2 and as well retrieved from the probability maps with thresholds at 50% confidences. These are volumes with binary values 1 and 0.

        The Rat Atlas is a three dimensional (3D) computerized map of rat brain anatomy created with digital imaging techniques. Electronic sharing and interactive use are benefits afforded by a digital format, but the foremost advantage of this 3D map is its whole brain integrated representation of rat in situ neuroanatomy.

        Cryo atlas:
        Images have been registered to an MRI atlas generated from 357 male and female vervets three years of age or older and reflect the mean affine size and shape of the population, not those of the specific animal from which these images were generated. "MRI stereotaxic coordinates" are relative to the mean MRI atlas anterior commissure, which is anterior to the anterior commissure of the particular animal shown here. "This atlas" coordinates are slice numbers in the high resolution atlas shown here (0.1667 mm thick slices). "MRI atlas" coordinates are slice numbers in the corresponding MRI atlas (0.5 mm thick slices). Click on listed coordinates to modify them.

        Average MRI atlas:
        Data is from a population of 357 Chlorocebus aethiops sabaeus male and female monkeys. The images have been registered and scaled to reflect the mean affine size and shape of the population. Ten animals were with structural abnormalities were omitted in generating the intensity averaged images shown here. All animals were three years of age or older. "MRI stereotaxic coordinates" are relative to the mean MRI atlas anterior commissure. "This atlas" coordinates are slice numbers in the (0.5 mm thick slices) atlas shown here. "Brain atlas" coordinates are slice numbers in the corresponding high resolution (0.1667 mm) anatomic atlas. Please click on listed coordinates to modify them.


        ANATOMY 3D ATLAS

        ANATOMY 3D ATLAS allows you to study human anatomy in an easy and interactive way. Through a simple and intuitive interface it is possible to observe every anatomical structure from any angle. Highly detailed 3D models, with textures up to 4k resolution, enable to examine the shape of each structure of the human body with great depth.

        Systems: Musculoskeletal, Cardiovascular, Nervous, Respiratory, Digestive, Urogenital (male and female), Endocrine, Lymphatic, Eye and ear.

        This application is aimed at medical students, doctors, physiotherapists, paramedics, nurses, athletic trainers and in general anyone interested in deepening their knowledge of human anatomy.

        This app is a fantastic tool to complement classic human anatomy books.

        TRY THE APP

        This app is freely downloadable, however an in-app purchase is required to unlock all the contents. Some of the contents are always freely accessible enabling you to try the app properly.


        Complete Heart

        Complete Heart is another free 3D anatomy app for Windows 10. As the name suggests, you can view and study heart anatomy in 3D using this app. You can view and learn about cardiovascular system, pericardium, major arteries, great vessels, etc. As you select a part, it displays the name of selected part. You can rotate and zoom the view to see the heart in 3D. It lets you enable/disable different layers of the heart. It also provides an inbuilt search feature to look for heart component.

        Note: In the free version of this app, rest of the features are disabled. You need to upgrade to its premium version in order to unlock all its features.


        Atlas from human brain structures to 3D coordinates? - Biology

        This brain cell database contains a survey of biological features derived from single cell data, from both human and mouse. It is part of a multi-year project to create a census of cells in the mammalian brain.

        The database contains electrophysiological, morphological, and transcriptomic data measured from individual cells, as well as models simulating cell activity. Thus far, data generation has focused on select areas of cerebral cortex, and thalamic neurons.

        Browse electrophysiological response data and reconstructed neuronal morphologies using the Cell Feature Search tool. Single cell gene expression data is described on the RNA-Seq Data page.

        Use the Allen Software Development Kit (SDK) to programmatically access and analyze raw data, and to run models.

        Data can be downloaded by selecting individual experiments in the Cell Feature Search tool, by accessing transcriptomic RNA-Seq files, or through the Allen SDK or API.

        Single Cells from Human Brain

        Cells are acquired from donated ex vivo brain tissue dissected from temporal or frontal lobes, based on anatomical annotations described in The Allen Human Brain Reference Atlas. For electrophysiological and morphological analyses in the cortex, cells are selected based on soma shape and laminar location.

        For transcriptomic analysis, individual layers of cortex are dissected, and neuronal nuclei are isolated. Laminar sampling is guided by the relative number of neurons present in each layer.

        Single Cells from Mouse Brain

        Cells are acquired from selected brain areas in the adult mouse. Cells are identified for isolation using transgenic mouse lines harboring fluorescent reporters, with drivers that allow enrichment for cell classes based on marker genes. For electrophysiological and morphological analyses, excitatory cells with layer-enriched distribution and inhibitory cells expressing canonical markers were isolated. Brain areas selected for analysis include subregions from visual cortex, motor cortex and anterior lateral motor cortex (ALM), in the secondary motor area (MOs). Subregions from visual cortex (secondary visual areas) are also included.

        For transcriptomic analysis, regional and laminar dissections were performed on specimens from pan-neuronal, pan-excitatory, and pan-inhibitory transgenic lines, to sample comprehensively. Data from the lateral geniculate nucleus (LGd) is also included.


        Atlas from human brain structures to 3D coordinates? - Biology

        The Allen Brain Explorer (beta) is an application that allows users to browse multimodal datasets in an annotated 3D spatial framework. The most recent release of this application is an integrated web-based navigator, allowing users to explore the Allen Mouse Brain Connectivity Atlas projection data and Allen Reference Atlas (ARA) in a standardized coordinate space.

        The Brain Explorer 2 software is a desktop application for viewing the Allen Mouse Brain Connectivity Atlas projection data and the Allen Mouse Brain Atlas gene expression data in the framework of the Allen Reference Atlas (ARA). This downloadable software will be discontinued in 2019, as improved functionality and new features will be available via an integrated web-based platform. Ongoing updates to this software will be discontinued after that time.

        Using the Brain Explorer 2 software, you can:

        • View a fully interactive version of the ARA in 3-D.
        • View projection and gene expression data in 3-D at 200 μm 3 resolution.
        • View projection and expression data from multiple image series superimposed on each other in 3-D.
        • Navigate the high-resolution 2-D projection and ISH images using the 3-D model.
        • Link to associated projection and gene metadata in the Allen Mouse Brain Atlas web application.

        The 3-D data shown in the Brain Explorer 2 software is generated from the same process employed in the search algorithms on the Allen Mouse Brain Connectivity Atlas web site see the Brain Explorer paper or the informatics white paper for more information.

        After installing the application, you can view projection data by selecting an anatomic structure in the application and searching from the Atlas menu, or you can perform a search from the Projection tab on this website. You can view gene expression data by performing a gene search from the mouse ISH website or from within the application main window. Please see the documentation for more information.

        Please verify your system meets the requirements before installing.

        Windows Minimum Configuration

        • Operating System: Microsoft Windows 7
        • CPU: Intel Core Duo or AMD 1.8GHz
        • System Memory: 1GB
        • Graphics Card: Hardware 3D OpenGL accelerated AGP or PCI Express with 64MB RAM
        • Screen: 1024x768, 32-bit true color
        • Hard Disk: 200MB free space

        Note: Brain Explorer is known to work with the following video chipsets: nVidia GeForce 9400/9600, nVidia Quadro FX 1800/3800/5600, AMD Radeon 9600, AMD Radeon HD 3200/4550, Intel Q35/Q45 Express.

        Important: Please install the latest drivers for your video card for best compatibility and performance.

        Mac Minimum Configuration

        • Operating System: OS X 10.6.8
        • CPU: Intel 1.8GHz
        • System Memory: 1GB
        • Graphics Card: 3D-capable with 64MB RAM
        • Screen: 1024x768, 32-bit millions of colors
        • Hard Disk: 200MB free space

        Note: Please install the latest system updates from Apple to ensure you have the latest video card drivers.


        Contents

        Anterior arch Edit

        The anterior arch forms about one-fifth of the ring: its anterior surface is convex, and presents at its center the anterior tubercle for the attachment of the Longus colli muscles and the anterior longitudinal ligament posteriorly it is concave, and marked by a smooth, oval or circular facet (fovea dentis), for articulation with the odontoid process (dens) of the axis.

        The upper and lower borders respectively give attachment to the anterior atlantooccipital membrane and the anterior atlantoaxial ligament the former connects it with the occipital bone above, and the latter with the axis below. [3]

        Posterior arch Edit

        The posterior arch forms about two-fifths of the circumference of the ring: it ends behind in the posterior tubercle, which is the rudiment of a spinous process and gives origin to the Recti capitis posteriores minores and the ligamentum nuchae. The diminutive size of this process prevents any interference with the movements between the atlas and the skull.

        The posterior part of the arch presents above and behind a rounded edge for the attachment of the posterior atlantooccipital membrane, while immediately behind each superior articular process is the superior vertebral notch (sulcus arteriae vertebralis). This is a groove that is sometimes converted into a foramen by ossification of the posterior atlantooccipital membrane to create a delicate bony spiculum which arches backward from the posterior end of the superior articular process. This anatomical variant is known as an arcuate foramen.

        This groove transmits the vertebral artery, which, after ascending through the foramen in the transverse process, winds around the lateral mass in a direction backward and medially to enter the vertebrobasilar circulation through the foramen magnum it also transmits the suboccipital nerve (first spinal nerve)

        On the under surface of the posterior arch, behind the inferior articular facets, are two shallow grooves, the inferior vertebral notches. The lower border gives attachment to the posterior atlantoaxial ligament, which connects it with the axis.

        Lateral masses Edit

        The lateral masses are the most bulky and solid parts of the atlas, in order to support the weight of the head.

        Each carries two articular facets, a superior and an inferior.

        • The superior facets are of large size, oval, concave, and approach each other in front, but diverge behind: they are directed upward, medially, and a little backward, each forming a cup for the corresponding condyle of the occipital bone, and are admirably adapted to the nodding movements of the head. Not infrequently they are partially subdivided by indentations which encroach upon their margins.
        • The inferior articular facets are circular in form, flattened or slightly convex and directed downward and medially, articulating with the axis, and permitting the rotatory movements of the head.

        Vertebral foramen Edit

        Just below the medial margin of each superior facet is a small tubercle, for the attachment of the transverse atlantal ligament which stretches across the ring of the atlas and divides the vertebral foramen into two unequal parts:

        • the anterior or smaller receiving the odontoid process of the axis
        • the posterior transmitting the spinal cord (medulla spinalis) and its membranes

        This part of the vertebral canal is of considerable size, much greater than is required for the accommodation of the spinal cord.

        Transverse processes Edit

        The transverse processes are large they project laterally and downward from the lateral masses, and serve for the attachment of muscles which assist in rotating the head. They are long, and their anterior and posterior tubercles are fused into one mass the foramen transversarium is directed from below, upward and backward.

        Development Edit

        The atlas is usually ossified from three centers.

        Of these, one appears in each lateral mass about the seventh week of fetal life, and extends backward at birth, these portions of bone are separated from one another behind by a narrow interval filled with cartilage.

        Between the third and fourth years they unite either directly or through the medium of a separate center developed in the cartilage.

        At birth, the anterior arch consists of cartilage in this a separate center appears about the end of the first year after birth, and joins the lateral masses from the sixth to the eighth year.

        The lines of union extend across the anterior portions of the superior articular facets.

        Occasionally there is no separate center, the anterior arch being formed by the forward extension and ultimate junction of the two lateral masses sometimes this arch is ossified from two centers, one on either side of the middle line.

        Muscular attachments Edit

        Transverse processes Edit

          – occipital bone (inferior surface of the base) – occipital bone (beneath the jugular process) – occipital bone (between the superior and inferior nuchal lines)
          (part) – spinous processes of T02–T05 (part) – superior part of medial border of the scapula – transverse process of the axis (posterior tubercle) – transverse process of the axis (anterior tubercle)

        Posterior tubercle Edit

          – occipital bone (medial part of the interior nuchal line, and the surface between it and the foramen magnum)

        Anterior arch Edit

        A break in the first vertebra is referred to as a Jefferson fracture.

        Craniocervical junction misalignment is also suspected as a factor in neurodegenerative diseases where altered CSF flow plays a part in the pathological process.

        Hyperextension (Whiplash) Injury

        A rear-end traffic collision or a poorly performed rugby tackle can both result in the head being whipped back on the shoulders, causing whiplash. In minor cases, the anterior longitudinal ligament of the spine is damaged which is acutely painful for the patient.

        In more severe cases, fractures can occur to any of the cervical vertebrae as they are suddenly compressed by rapid deceleration. Again, since the vertebral foramen is large there is less chance of spinal cord involvement.

        The worst-case scenario for these injuries is that dislocation or subluxation of the cervical vertebrae occurs. This often happens at the C2 level, where the body of C2 moves anteriorly with respect to C3. Such an injury may well lead to spinal cord involvement, and as a consequence quadriplegia or death may occur. More commonly, subluxation occurs at the C6/C7 level (50% of cases).

        Shape and position of atlas (shown in red), from above. The skull is shown in semi-transparent.